Analysis
## Loading required package: ggplot2
## Loading required package: plyr
## Runing PhenoGraph...
## Run Rphenograph starts:
## -Input data of 43333 rows and 17 columns
## -k is set to 30
## Finding nearest neighbors...DONE ~ 2.316 s
## Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 16.681 s
## Build undirected graph from the weighted links...DONE ~ 3.846 s
## Run louvain clustering on the graph ...DONE ~ 3.885 s
## Run Rphenograph DONE, totally takes 26.728s.
## Return a community class
## -Modularity value: 0.863889
## -Number of clusters: 23 DONE!
## Runing t-SNE...with seed 42 DONE
## Runing PhenoGraph...
## Run Rphenograph starts:
## -Input data of 138570 rows and 17 columns
## -k is set to 30
## Finding nearest neighbors...DONE ~ 9.945 s
## Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 52.86 s
## Build undirected graph from the weighted links...DONE ~ 13.499 s
## Run louvain clustering on the graph ...DONE ~ 15.151 s
## Run Rphenograph DONE, totally takes 91.455s.
## Return a community class
## -Modularity value: 0.8810334
## -Number of clusters: 33 DONE!
## Runing t-SNE...with seed 42 DONE
Starting from PBMCs, I think
TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated

Starting from Dendritic, I think
TSNE results

TSNE results, colored by Phenograph clusters detected

TSNE results, colored by manual gates

TSNE results, Manually gated
